Reproducible Research with and : Workflows for data, projects and publications

Landscape 2024 masterclass

Ben Black

Planning of Landscape and Urban Systems (PLUS), ETH Zurich

Manuel Kurmann

Planning of Landscape and Urban Systems (PLUS), ETH Zurich

Nivedita Harisena

Planning of Landscape and Urban Systems (PLUS), ETH Zurich

Maarten Van Strien

Planning of Landscape and Urban Systems (PLUS), ETH Zurich

September 13, 2024

Quarto

Quarto

  • An open source scientific and technical publishing system

  • Integrates code in multiple programming languages, written material, and interactive visual components

  • Produces a range of document formats including HTML, PDF, and Word

  • Developed by Posit the same company that created Rstudio.

Quarto

  • Quarto website presents many examples of it’s applications
  • We will focus on some of it’s key uses and features that are relevant for academics and producing reproducible research.
    • Academic manuscripts
    • Presentations
    • Websites
    • Interactive dashboards
    • Data exploration and visualization

Quarto

Writing academic manuscripts

How many programs do you currently use when writing academic papers?

A common workflow of academic papers [1]

Quarto

Writing academic manuscripts

Quarto solves this problem by allowing you to write full academic manuscripts from start to finish including text, code, and visualizations in a single document:

Quarto

Writing academic manuscripts

Key benefits:

  • Figures and tables are dynamically updated as your code changes

  • Supports code in R, Python and Julia as well as LaTeX and Markdown content

  • Easy Cross-referencing capability for figures, tables, and sections

  • Documents can be rendered as Word, PDF, or HTML

  • Include Citations and bibliographies using Crossref, DataCite, PubMed and direct integration with Zotero

  • Quarto’s .qmd files can be edited with various code/text editors (VS Code, RStudio etc.)

More reproducible as it allows others to use your underlying manuscript file in combination with your data to directly re-create your results.

Quarto

Presentations

Several formats: RevealJS, Microsoft Powerpoint and Beamer using a common syntax.

Useful features:

  • Modern themes with functionality to publish your own theme.

  • Interactive content: Executable code blocks, graphs, maps

  • Dynamic resizing of content depending on screen size

  • Functionality for slide notes, automatic transitions, timers etc.

  • Easy export to PDF or HTML

  • Similar to manuscripts code-based content is dynamically updated.

Quarto

Websites

Websites to act as guides, tutorials or teaching materials:

Quarto

Websites

Personal websites to share publications and presentations:

Quarto

Websites

Websites for research projects to share progress and results:

Quarto

Dashboards

  • Arrange multiple interactive or static components in a single page with a highly customizable layout.
  • Components can include text summaries, tables, plots, maps and more.
  • Uses: Collect feedback on aspects of your research during development or present your results in a visually appealing way.

Gapminder dashboard from JJallaire

Quarto

Data exploration and visualization

Many options for interactive data visualisations, tables and diagrams using:

Let’s take another 10 minute break!

Now it’s your turn!

Q&A + feedback

Bibliography

1.
Lusseau D, Douglas A, Roos D, Mancini F, Couto A (2024) An introduction to r